It is for the first time the agency has offered a possible price tag in the high-profile case, the Washington Post reported.
Director James Comey did not offer a precise dollar figure, saying it cost “a lot” to get into the phone.
Comey said the cost of the tool was “more than I will make in the remainder of this job, which is seven years and four months, for sure.”
Comey is paid at the rate set for Level II of the executive salary schedule. That means he makes $185,100 a year, under the pay schedules that went into effect this year.
As a result, Comey’s remarks strongly implied that the bureau paid at least $1.3 million to get onto Syed Rizwan Farook’s iPhone.
Farook, with his wife Tashfeen Malik, killed 14 people in the December 2 terror attack in San Bernardino.
“But it was, in my view, worth it,” the FBI director said of what it cost to access the phone’s data.
Federal authorities have not publicly revealed who helped the FBI unlock the iPhone, which was at the center of an extended fight between the government and iPhone maker Apple.
The Justice Department had maintained that only Apple could help it access the phone without erasing all of its data before abruptly saying it had gotten help from an outside party and no longer needed Apple’s assistance.
According to people familiar with the issue, the FBI cracked the phone with the help of professional hackers who were paid a one-time flat fee.
Law enforcement officials have said recently that the FBI has found no links to foreign terrorists on the phone, though they are still hoping that geolocation data on the device could help reveal what the attackers did during an 18-minute period after the shooting.
Earlier this month, Comey had said the government was considering telling Apple how it accessed the phone, though he acknowledged if that happened, the technology giant would fix the flaw and close off that avenue.
Comey said the tool would only work on a “narrow slice” of devices, saying he was “pretty confident” it would not work on newer models.
Comey conceded Thursday that the tool would work only on an iPhone 5c running iOS 9.
In part because of the price tag, Comey said he hoped the government could figure out a solution to access other, more current phones without having to make mass appeals to the tech industry for some kind of hack.
He noted that there were 18,000 law enforcement agencies across the US that might want to access phones and could not afford what the FBI paid to access the San Bernardino phone.
The FBI’s total budget for fiscal year 2016 was more than $8.7 billion, and the bureau requested more than $9.5 billion for fiscal year 2017.